Ancestral Genome Reconstruction on Whole Genome Level

Current Genomics
Bing FengJijun Tang

Abstract

Comparative genomics, evolutionary biology, and cancer researches require tools to elucidate the evolutionary trajectories and reconstruct the ancestral genomes. Various methods have been developed to infer the genome content and gene ordering of ancestral genomes by using such genomic structural variants. There are mainly two kinds of computational approaches in the ancestral genome reconstruction study. Distance/event-based approaches employ genome evolutionary models and reconstruct the ancestral genomes that minimize the total distance or events over the edges of the given phylogeny. The homology/adjacency-based approaches search for the conserved gene adjacencies and genome structures, and assemble these regions into ancestral genomes along the internal node of the given phylogeny. We review the principles and algorithms of these approaches that can reconstruct the ancestral genomes on the whole genome level. We talk about their advantages and limitations of these approaches in dealing with various genome datasets, evolutionary events, and reconstruction problems. We also talk about the improvements and developments of these approaches in the subsequent researches. We select four most famous and powerful approaches from bo...Continue Reading

Citations

Nov 11, 2017·Scientific Reports·Bing FengJijun Tang

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Software Mentioned

InferCARsPro
BPAnalysis
MGRA
GRAPPA
PMAG
MLGO
InferCARs
Gapped
Concorde
MGAR2

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